Comments
-If you open up the Pokemon Raptor folder and use Vista's 'Show Hidden Folders' option, there's a folder called PBS. If you open that up, there's various .txt documents that give helpful information about the game. For example, pokemon.txt is like a Pokedex which will tell you how to evolve every Pokemon and the levels that they learn new moves. (This is how I knew how to evolve my Rhydon into a Rhyperior through Happiness.) I like how a lot of 'Trade/Item Evolutions' were changed to 'Move Evolutions'. Encounter.txt is also helpful, because it tells you what Pokemon are located on each map. (This is how I knew that I could catch Bagons at Terra Cave, an event map.)

-I loved how the legendaries were scattered throughout the world after you beat the game. Lugia was hidden in a good spot!

-Are there supposed to be two Mewtwo's after you beat the game?

Spoiler:

I found one in Destiny Cave and another in the Krypton Factory Underground.

-Darkrai is kind of pointless since when you catch it, it has Dream Eater and Nightmare but doesn't learn any moves that can induce sleep.

-After catching/killing Froslass or Rotom in their events, the game crashes.

-Where do we get Manaphy? Maybe I haven't found it yet. I got Phione though.

-Heatran doesn't disappear after you battle it. This is useful for training Pokemon though, especially those that know Earthquake.

-Mew is located in Sootopolis City but you can't get to it since you're trapped at the PokeCenter entrance when you fly there. This also means that we cannot access Millennium Cave. I suppose that's the location of Rayquaza?

-It's important to get Lucky Eggs and Amulet Coins from the Mining Mini-Game at Mastric City. The enemy Pokemon increase in level very quickly, so Lucky Eggs help you keep up without wasting too much time training. You need so many Ultra Balls for Legendaries, so Amulet Coin helps you afford them.

-Does Breeding work? I tried to breed Larvitar and Rhyhorn since they're in the same Egg Group, but the Old Man says they aren't compatible. Breeding would give Pokemon better move pools through Egg Moves since there's a lack of TMs.

-Entei and Raikou have Roar, making them really difficult to catch since they'll end the battle in a few turns. Suicune is easier since it doesn't have Roar.

-People on this thread said that Eevee evolves into Umbreon with a Moon Stone. Eevee evolves into Umbreon or Espeon based on its gender at level 16, not with a Stone.

-A Pokemon with the Trace ability will crash the game if it encounters a Pokemon without an ability.

-You need to be careful where you save. Saving right in front of Legendaries not always a good idea; if you're in an event and you save, you're most likely stuck in that event. This could be a problem if you're about to face a Legendary with little to no Ultra Balls and a weakened Pokemon party. (I was stuck fighting the Lvl 60 Giratina with 2 Pokemon and less than 10 Ultra Balls. It took a lot of resets to finally catch it.) Some events are difficult since you fight multiple legendaries without having a chance to heal or restock Ultra Balls in between. (e.g. Groudon/Kyogre and Regi/Regigigas)

-If anyone needs an HM Mule, Tropius is great. It can learn Cut/Rock Smash/Fly/Strength. However, you only need Cut once and Strength only a few times. (You can walk through boulders sometimes, such as in the Tree of Life.) Flash doesn't seem to be needed at all.

-Thief/Covet/Item Swap/etc permanently remove your item after the battle. This is annoying when you lose a precious Lucky Egg/Amulet Coin/Choice Band/etc.

-When you dive, if you hit "A", it automatically asks if you want to resurface.

Spoiler:

This gave me trouble when I tried to challenge Lugia and pick up the Phione egg.

-I don't think any of the Flutes work.

-There's only 117 trainers in the game. This is very few compared to the actual Pokemon games which have 300+. As a result, you'll be training on wild Pokemon most of the time, which give less EXP than trainer Pokemon. However, I think 117 is definitely enough because you can rebattle the Gaia Wings once you beat the game to train with EXP Share. It must be tedious to add trainers, so I don't blame you.

-The Swimmer on Route 20 crashes the game. However, the map is changed so you can't encounter the Swimmer after you beat the game which is good.

-Is the EV system implemented or not? I can't tell. When I level up, the stats shown are different than the stats when you view the Pokemon's summary.

-Overall, great game! It's very complete for a fan-made game. Adding 4th Generation moves would be great addition though!